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A previously developed spectrometer for broadband electron paramagnetic resonance (EPR) spectroscopy of dilute randomly oriented systems has been considerably modified to extend the frequency reach down to the hundred MHz range and to boost concentration sensitivity by 1 to 2 orders of magnitude. The instrument is now suitable for the study of biological systems in particular metalloproteins. As a proof of concept, examples from the class of low-spin ferric hemoproteins are studied in terms of frequency-dependent changes in their EPR spectra. Mono-heme cytochrome c EPR is determined by g-strain over a wide frequency range, whereas a combination of unresolved ligand hyperfine interaction and concentration-dependent intermolecular dipolar interaction becomes dominant at very low frequencies. In the four heme containing cytochrome c3, g-strain combines with intramolecular dipolar interaction over the full-studied frequency range of 0.23-12.0 GHz. It is concluded that the point-dipole approach is inappropriate to describe magnetic interactions between low-spin ferric heme systems and that a body of literature on redox interactions in multi-heme proteins will be affected by this conclusion.

Directional internal rotation in molecular systems, generally controlled by chirality, is known to occur in natural and artificial systems driven by light or fueled chemically, but spontaneous directional molecular rotation is believed to be forbidden. We have designed a molecular rotor, whereby ferrocene and triptycene linked by a methylene bridge provide two rotational degrees of freedom. On the basis of experimental observations, in conjunction with computational data, we show that the two different modes of rotation are strongly coupled and the spatial orientation of the bistable ferrocene moiety controls the barrier to its own rotation about the triptycene axis. It is proposed that the barrier to clockwise 120° rotation across each individual triptycene blade is lower in the M-enantiomer and for counterclockwise 120° rotation, it is lower in its P-counterpart. These findings demonstrate the possibility of locally preferred thermal directional intramolecular rotation for each dynamically interconverting enantiomer.

We present a theoretical study of a two-photon absorption (2PA) process in dipolar and quadrupolar systems containing two BF2 units. For this purpose, we considered 13 systems studied by Ponce-Vargas et al. [J. Phys. Chem. B2017, 121, 10850−1085829136383] and performed linear and quadratic response theory calculations based on the RI-CC2 method to obtain the 2PA parameters. Furthermore, using the recently developed generalized few-state model, we provided an in-depth view of the changes in 2PA properties in the molecules considered. Our results clearly indicate that suitable electron-donating group substitution to the core BF2 units results in a large red-shift of the two-photon absorption wavelength, thereby entering into the desired biological window. Furthermore, the corresponding 2PA strength also increases significantly (up to 30-fold). This makes the substituted systems a potential candidate for biological imaging.

Moving beyond the six-atomic benchmark systems, we discuss the new age and future of first-principles reaction dynamics, which investigates complex, multichannel chemical reactions. We describe the methodology starting from the benchmark ab initio characterization of the stationary points, followed by full-dimensional potential energy surface (PES) developments and reaction dynamics computations. We highlight our composite ab initio approach providing benchmark stationary-point properties with subchemical accuracy, the Robosurfer program system enabling automatic PES development, and applications for the Cl + C2H6, F + C2H6, and OH- + CH3I post-six-atom reactions focusing on ab initio issues and their solutions as well as showing the excellent agreement between theory and experiment.

The properties of a material depend on how its atoms are arranged, and predicting these arrangements from first principles is a longstanding challenge. Orbital-free density functional theory provides a quantum-mechanical model based solely on the electron density, not individual wave functions. The resulting speedups make it attractive for random structure searching, whereby random configurations of atoms are relaxed to local minima in the energy landscape. We use this strategy to map the low-energy crystal structures of Li, Na, Mg, and Al at zero pressure. For Li and Na, our searching finds numerous close-packed polytypes of almost-equal energy, consistent with previous efforts to understand their low-temperature forms. For Mg and Al, the searching identifies the expected ground state structures unambiguously, in addition to revealing other low-energy structures. This new role for orbital-free density functional theory-particularly as continued advances make it accurate for more of the periodic table-will expedite crystal structure prediction over wide ranges of compositions and pressures.

A dispersion function Das in the form of a damped atom–atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised Das function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original Das. A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts.

Independently of the preparation method, for cluster cations of aliphatic amino acids, the protonated form MnH+ is always the dominant species. This is a surprising fact considering that in the gas phase, they dissociate primarily by the loss of 45 Da, i.e., the loss of the carboxylic group. In the present study, we explore the dissociation dynamics of small valine cluster cations Mn+ and their protonated counterparts MnH+ via collision-induced dissociation experiments and ab initio calculations with the aim to elucidate the formation of MnH+-type cations from amino acid clusters. For the first time, we report the preparation of valine cluster cations Mn+ in laboratory conditions, using a technique of cluster ion assembly inside He droplets. We show that the Mn+ cations cooled down to He droplet temperature can dissociate to form both Mn-1H+ and [Mn-COOH]+ ions. With increasing internal energy, the Mn-1H+ formation channel becomes dominant. Mn-1H+ ions then fragment nearly exclusively by monomer loss, describing the high abundance of protonated clusters in the mass spectra of amino acid clusters.

Absorption and magnetic circular dichroism (MCD) spectra have been measured and theoretically simulated for a series of palladium octaethylporphyrins substituted at the meso positions with phenyl groups (n = 0–4). Analysis of the spectra included the perimeter model and time-dependent density functional theory (TDDFT) calculations. With the increasing number of phenyl substituents, the molecule is transformed from a positive hard (ΔHOMO > ΔLUMO) to a soft (ΔHOMO ≈ ΔLUMO) chromophore. This is manifested by a drastic decrease of the absorption intensity in the 0–0 region of the Q-band and by the strongly altered ratio of MCD intensities in the Q and Soret regions. Such behavior can be readily predicted using perimeter model, by analyzing frontier orbital shifts caused by various perturbations: alkyl and aryl substitution, insertion of a metal, and deviations from planarity. TDDFT calculations confirm the trends predicted by the perimeter model, but they fail in cases of less symmetrical derivatives to properly reproduce the MCD spectra in the Soret region. Our results confirm the power of the perimeter model in predicting absorption and MCD spectra of large organic molecules, porphyrins in particular. We also postulate, contrary to previous works, that the isolated porphyrin dianion is not a soft chromophore, but rather a strongly positive-hard one.

Recent electrochemical experiments have shown that the reduction of O2 can be driven backward to water oxidation, which is the first case that has been successfully demonstrated for an enzyme. To understand this ability of the enzyme, both the forward reduction and backward oxidation have been studied here. For the forward reaction, a mechanism similar to earlier studies was obtained. All steps of the full catalytic cycle were obtained for the first time, and it was shown that the explicit reduction steps contribute significantly to the rate-limiting step of the O–O bond cleavage. For the backward oxidation reaction, it was found that the mechanism of the O–O bond formation is not just the reverse of the reduction step where the O–O bond is cleaved for a protonated peroxide. The formation of two fully deprotonated oxo groups was found to be important, which leads to a large radical character for one of the oxo groups. For this possibility, it is important that the pKa of the water bound to the cofactor is quite high.

The Waddington mechanism, or the Waddington-type reaction pathway, is crucial for low-temperature oxidation of both alkenes and alcohols. In this study, the Waddington mechanism in the oxidation chemistry of butene and butanol isomers was systematically investigated. Fundamental quantum chemical calculations were conducted for the rate constants and thermodynamic properties of the reactions and species in this mechanism. Calculations were performed using two different ab initio solvers: Gaussian 09 and Orca 4.0.0, and two different kinetic solvers: PAPR and MultiWell, comprehensively. Temperature- and pressure-dependent rate constants were performed based on the transition state theory, associated with the Rice Ramsperger Kassel Marcus and master equation theories. Temperature-dependent thermochemistry (enthalpies of formation, entropy, and heat capacity) of all major species was also conducted, based on the statistical thermodynamics. Of the two types of reaction, dissociation reactions were significantly faster than isomerization reactions, while the rate constants of both reactions converged toward higher temperatures. In comparison, between two ab initio solvers, the barrier height difference among all isomerization and dissociation reactions was about 2 and 0.5 kcal/mol, respectively, resulting in less than 50%, and a factor of 2-10 differences for the predicted rate coefficients of the two reaction types, respectively. Comparing the two kinetic solvers, the rate constants of the isomerization reactions showed less than a 32% difference, while the rate of one dissociation reaction (P1 ↔ WDT12) exhibited 1-2 orders of magnitude discrepancy. Compared with results from the literature, both reaction rate coefficients (R4 and R5 reaction systems) and species' thermochemistry (all closed shell molecules and open shell radicals R4 and R5) showed good agreement with the corresponding values obtained from the literature. All calculated results can be directly used for the chemical kinetic model development of butene and butanol isomer oxidation.

As a key diagnostic property of benzenoids and other polycyclic hydrocarbons, induced ring current has inspired diverse approaches for calculation, modeling, and interpretation. Grid-based methods include the ipsocentric ab initio calculation of current maps, and its surrogate, the pseudo-π model. Graph-based models include a family of conjugated-circuit (CC) models and the molecular-orbital Huckel-London (HL) model. To assess competing claims for physical relevance of derived current maps for benzenoids, a protocol for graph-reduction and comparison was devised. Graph reduction of pseudo-π grid maps highlights their overall similarity to HL maps, but also reveals systematic differences. These are ascribed to unavoidable pseudo-π proximity limitations for benzenoids with short nonbonded distances, and to poor continuity of pseudo-π current for classes of benzenoids with fixed bonds, where single-reference methods can be unreliable. Comparison between graph-based approaches shows that the published CC models all shadow HL maps reasonably well for most benzenoids (as judged by L1-, L2-, and L∞-error norms on scaled bond currents), though all exhibit physically implausible currents for systems with fixed bonds. These comparisons inspire a new combinatorial model (Model W) based on cycle decomposition of current, taking into account the two terms of lowest order that occur in the characteristic polynomial. This improves on all pure-CC models within their range of applicability, giving excellent adherence to HL maps for all Kekulean benzenoids, including those with fixed bonds (halving the rms discrepancy against scaled HL bond currents, from 11% in the best CC model, to 5% for the set of 18 360 Kekulean benzenoids on up to 10 hexagonal rings). Model W also has excellent performance for open-shell systems, where currents cannot be described at all by pure CC models (4% rms discrepancy against scaled HL bond currents for the 20112 non-Kekulean benzenoids on up to 10 hexagonal rings). Consideration of largest and next-to-largest matchings is a useful strategy for modeling and interpretation of currents in Kekulean and non-Kekulean benzenoids (nanographenes).

Quasi-classical direct dynamics simulations, performed with the B3LYP-D3/cc-pVDZ electronic structure theory, are reported for vibrational relaxation of the three NH stretches of the -NH3+ group of protonated tryptophan (TrpH+), excited to the n = 1 local mode states. The intramolecular vibrational energy relaxation (IVR) rates determined for these states, from the simulations, are in good agreement with the experiment. In accordance with the experiment, IVR for the free NH stretch is slowest, with faster IVR for the remaining two NH stretches which have intermolecular couplings with an O atom and a benzenoid ring. For the free NH and the NH coupled to the benzenoid ring, there are beats (i.e., recurrences) in their relaxations versus time. For the free NH stretch, 50% of the population remained in n = 1 when the trajectories were terminated at 0.4 ps. IVR for the free NH stretch is substantially slower than for the CH stretch in benzene. The agreement found in this study between quasi-classical direct dynamics simulations and experiments indicates the possible applicability of this simulation method to larger biological molecules. Because IVR can drive or inhibit reactions, calculations of IVR time scales are of interest, for example, in unimolecular reactions, mode-specific chemistry, and many photochemical processes.

Accurate predictions of hyperfine structure (HFS) constants are important in many areas of chemistry and physics, from the determination of nuclear electric and magnetic moments to benchmarking of new theoretical methods. We present a detailed investigation of the performance of the relativistic coupled cluster method for calculating HFS constants within the finite-field scheme. The two selected test systems are 133Cs and 137BaF. Special attention has been paid to construct a theoretical uncertainty estimate based on investigations on basis set, electron correlation and relativistic effects. The largest contribution to the uncertainty estimate comes from higher order correlation contributions. Our conservative uncertainty estimate for the calculated HFS constants is ∼5.5%, while the actual deviation of our results from experimental values is

We present the first experimental study of the frontier orbitals in an ultrathin film of the novel hexa-carbene photosensitizer [Fe(btz)3]3+, where btz is 3,3′-dimethyl-1,1′-bis(p-tolyl)-4,4′-bis(1,2,3-triazol-5-ylidene). Resonant photoelectron spectroscopy (RPES) was used to probe the electronic structure of films where the molecular and oxidative integrities had been confirmed with optical and X-ray spectroscopies. In combination with density functional theory calculations, RPES measurements provided direct and site-selective information about localization and interactions of occupied and unoccupied molecular orbitals. Fe 2p, N 1s, and C 1s measurements selectively probed the metal, carbene, and side-group contributions revealing strong metal–ligand orbital mixing of the frontier orbitals. This helps explain the remarkable photophysical properties of iron-carbenes in terms of unconventional electronic structure properties and favorable metal–ligand bonding interactions—important for the continued development of these type of complexes toward light-harvesting and light-emitting applications.

Polycyclic hydrocarbons are often used to understand the electronic structure of nanographene systems. Among them, indeno[1,2b]fluorene and indeno[1,2c]fluorene isomers present a central p-quinodimethane unit leading to unique optical properties. In this work, we characterized the absorption spectra of indeno[1,2b]fluorene and [2,1-c]diindeno[n]thiophene derivatives with (spin-flip) simplified time-dependent density functional theory [(SF-)sTD-DFT] methods. Note that the SF-sTD-DFT level of theory allows a computationally efficient treatment for large diradicals. To interpret spectra, we implemented natural transition orbitals (NTOs) at both SF-sTD-DFT and sTD-DFT levels. This compact and method-independent representation of the electronic excitation provides a simple interpretation for the low-lying excited states of this set of molecules in terms of three different types of NTOs: "quinoid", "aromatic", and "π-bonded". When comparing with experiment, we found that only one molecule of this set is actually a high-spin triplet diradical. Others are almost closed-shell molecules with a very small contribution from a doubly excited configuration that only the spin-flip method could capture. The small amount of static correlation recovered by the spin-flip active space provides a linear relation between the first visible theoretical and experimental excitation energies among this set.

Photodissociation of vibrationally and electronically excited sulfur dimer molecules (S2) has been studied in a combined experimental and computational quantum chemistry study in order to characterize bound-continuum transitions. Ab initio quantum chemistry calculations are carried out to predict the potential energy curves, spin-orbit coupling, transition moments, and bound-continuum spectra of S2 for comparison with the experimental data. The experiment uses velocity map imaging to measure S-atom production following S2 photoexcitation in the ultraviolet region (320-205 nm). A pulsed electric discharge in H2S produces ground-state S2 X3ςg -(v = 0-15) as well as electronically excited singlet sulfur and b1ςg +(v = 0, 1), and evidence is presented for the production and photodissociation of S2 a1Δg. In a previous paper, we reported threshold photodissociation of S2X3ςg -(v = 0) in the 282-266 nm region. In the present study, S(3PJ) fine structure branching and angular distributions for photodissociation of S2 (X3ςg -(v = 0), a1Δg and b1ςg +) via the B″3IIu, B3ςu - and 11IIu excited states are reported. In addition, photodissociation of the X3ςg -(v = 0) state of S2 to the second dissociation limit producing S(3P2) + S(1D) is characterized. The present results on S2 photodynamics are compared to those of the well-studied electronically isovalent O2 molecule.

Energy minima on the potential energy surfaces of the ground and excited states have been characterized for three photoactive molecules that undergo excited-state intramolecular proton transfer: 3-hydroxychromone, N-salicylideneaniline, and 2-(2-hydroxyphenyl)benzothiazole. Both the CC2 method and the TDDFT methodology with different exchange-correlation (XC) functionals differing by the amount of Hartree-Fock (HF) exchange have been employed. Besides the analysis of the structures along the reaction paths, this study has compared the TDDFT and CC2 results to provide guidelines for selecting the best XC functionals. Several geometrical parameters as well as the excitation energies are found to vary monotonically with the amount of HF exchange. Systematically, this study has addressed the ground-state geometries, those of the excited states, and their variations upon excitation, showing that the M06 XC functional provides the closest agreement with the CC2 results. Still, large differences of geometries have been observed between the different levels of approximation, mostly for the excited states: (i) Not all methods locate the same number of minima, (ii) the bond length variations upon excitation might be reversed, and (iii) the H-bond network can be modified from one level to another, changing the keto/enol character. Moreover, TDDFT/M06 and B3LYP-35 vertical excitation energies are in good agreement with the CC2 values. All in all, these results call for being cautious when using these optimized geometries for predicting the spectroscopic signatures of these compounds to understand the processes that take place during photoexcitation.

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.